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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit 600a9e3c1d884e5cf106e4477c7b8223ef105cdb"
author iuc
date Thu, 29 Apr 2021 12:23:33 +0000
parents a4962f14d05d
children
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1 <?xml version="1.0"?>
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2 <macros>
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3 <token name="@TOOL_VERSION@">1.0.11</token>
1
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4 <token name="@VERSION_SUFFIX@">1</token>
0
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5 <token name="@PROFILE@">20.01</token>
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6 <xml name="requirements">
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">jasminesv</requirement>
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9 </requirements>
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10 </xml>
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11 <xml name="version_command">
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12 <version_command>jasmine</version_command>
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13 </xml>
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14 <xml name="citations">
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15 <citations>
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16 <citation type="bibtex">@online{jasmine,
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17 author = {Melanie Kirsche},
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18 title = {jasmine},
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19 year = 2021,
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20 url = {https://github.com/mkirsche/Jasmine},
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21 urldate = {2021-01-13}
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22 }</citation>
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23 </citations>
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24 </xml>
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25 <!--
a4962f14d05d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
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26 Command
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27 -->
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28 <token name="@REF_FASTA@"><![CDATA[
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29 #if $dup_to_ins.reference_source.reference_source_selector == 'history':
1
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30 #set reference = $dup_to_ins.reference_source.ref_file
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31 #set ext = $reference.ext
0
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32 #else:
1
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33 #set reference = $dup_to_ins.reference_source.ref_file.fields.path
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34 #set ext = $dup_to_ins.reference_source.ref_file.fields.path
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35 #end if
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36 #if $ext.endswith(".gz"):
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37 gunzip -c '$reference' > reference &&
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38 #else:
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39 ln -sf '$reference' reference &&
0
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40 #end if
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41 ]]></token>
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42
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43 <xml name="reference">
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44 <conditional name="reference_source">
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45 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
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46 <option value="cached">Use a built-in genome</option>
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47 <option value="history">Use a genome from history</option>
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48 </param>
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49 <when value="cached">
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50 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
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51 <options from_data_table="all_fasta">
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52 <filter type="sort_by" column="2"/>
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53 <validator type="no_options" message="No reference genomes are available"/>
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54 </options>
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55 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
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56 </param>
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57 </when>
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58 <when value="history">
1
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59 <param name="ref_file" type="data" format="fasta,fasta.gz,fastq,fastq.gz" label="Use the following dataset as the reference sequence" help="You can upload a FASTA or FASTQ sequence to the history and use it as reference"/>
0
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60 </when>
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61 </conditional>
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62 </xml>
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63 <!--
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64 Help
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65 -->
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66
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67 <token name="@WID@"><![CDATA[
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68 *Jasmine*, or Jointly Accurate Sv Merging with Intersample Network Edges is a tool used to merge structural variants (SVs) across samples. Each sample has a number of SV calls, consisting of position information (chromosome, start, end, length), type and strand information, and a number of other values. Jasmine represents the set of all SVs across samples as a network, and uses a modified minimum spanning forest algorithm to determine the best way of merging the variants such that each merged variants represents a set of analogous variants occurring in different samples.
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69 ]]></token>
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70 <token name="@REFERENCES@"><![CDATA[
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71 More information is available in the `github <https://github.com/mkirsche/Jasmine>`_.
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72 ]]></token>
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73 </macros>
1
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74